Chromosome 5 abnormalities, deletion of the long arm of chromosome 5 (del(5q)) or monosomy 5 (-5), arise in about 10% of myelodysplastic syndromes (MDS), either as the sole cytogenetic abnormality or as part of complicated karyotype, and has distinct clinical implications for MDS. However, the prognostic factors of MDS patients with chromosome 5 abnormalities are not determined yet. In this study, 183 Japanese MDS patients with chromosome 5 abnormalities were analyzed. Estimated incidence of del(5q) and 5q- syndrome among MDS patients was 8.4 and 1.3%, respectively. Significant shorter overall survival (OS) and leukemia-free survival (LFS) were observed in -5 patients than del(5q) patients. Among del(5q) patients, addition of monosomy 7 or complex karyotype with more than three abnormalities were significantly related to shorter OS. LFS of del(5q) patients was divided into two risk groups by international prognostic scoring system (IPSS): low/intermediate (Int)-1 and Int-2/high groups. LFS sorted by World Health Organization classification-based prognostic scoring system (WPSS) was also divided into two groups: very low/low/Int and high/very high, and WPSS was able to predict the outcome of del(5q) patients more clearly than IPSS. Together with additional cytogenetic data, WPSS might be useful for clinical decision making in MDS patients with del(5q).